Job ID = 1290599 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,427,736 reads read : 11,427,736 reads written : 11,427,736 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:19 11427736 reads; of these: 11427736 (100.00%) were unpaired; of these: 473668 (4.14%) aligned 0 times 9642211 (84.38%) aligned exactly 1 time 1311857 (11.48%) aligned >1 times 95.86% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1521602 / 10954068 = 0.1389 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 01 Jun 2019 21:53:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 01 Jun 2019 21:53:26: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:53:26: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 01 Jun 2019 21:53:27: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:53:27: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 01 Jun 2019 21:53:27: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:53:27: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:53:40: 1000000 INFO @ Sat, 01 Jun 2019 21:53:41: 1000000 INFO @ Sat, 01 Jun 2019 21:53:41: 1000000 INFO @ Sat, 01 Jun 2019 21:53:54: 2000000 INFO @ Sat, 01 Jun 2019 21:53:54: 2000000 INFO @ Sat, 01 Jun 2019 21:53:55: 2000000 INFO @ Sat, 01 Jun 2019 21:54:06: 3000000 INFO @ Sat, 01 Jun 2019 21:54:08: 3000000 INFO @ Sat, 01 Jun 2019 21:54:09: 3000000 INFO @ Sat, 01 Jun 2019 21:54:18: 4000000 INFO @ Sat, 01 Jun 2019 21:54:22: 4000000 INFO @ Sat, 01 Jun 2019 21:54:23: 4000000 INFO @ Sat, 01 Jun 2019 21:54:31: 5000000 INFO @ Sat, 01 Jun 2019 21:54:35: 5000000 INFO @ Sat, 01 Jun 2019 21:54:37: 5000000 INFO @ Sat, 01 Jun 2019 21:54:44: 6000000 INFO @ Sat, 01 Jun 2019 21:54:49: 6000000 INFO @ Sat, 01 Jun 2019 21:54:50: 6000000 INFO @ Sat, 01 Jun 2019 21:54:59: 7000000 INFO @ Sat, 01 Jun 2019 21:55:03: 7000000 INFO @ Sat, 01 Jun 2019 21:55:05: 7000000 INFO @ Sat, 01 Jun 2019 21:55:14: 8000000 INFO @ Sat, 01 Jun 2019 21:55:17: 8000000 INFO @ Sat, 01 Jun 2019 21:55:19: 8000000 INFO @ Sat, 01 Jun 2019 21:55:29: 9000000 INFO @ Sat, 01 Jun 2019 21:55:33: 9000000 INFO @ Sat, 01 Jun 2019 21:55:33: 9000000 INFO @ Sat, 01 Jun 2019 21:55:35: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:55:35: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:55:35: #1 total tags in treatment: 9432466 INFO @ Sat, 01 Jun 2019 21:55:35: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:55:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:55:35: #1 tags after filtering in treatment: 9432466 INFO @ Sat, 01 Jun 2019 21:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:55:35: #1 finished! INFO @ Sat, 01 Jun 2019 21:55:35: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:55:36: #2 number of paired peaks: 243 WARNING @ Sat, 01 Jun 2019 21:55:36: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 01 Jun 2019 21:55:36: start model_add_line... INFO @ Sat, 01 Jun 2019 21:55:36: start X-correlation... INFO @ Sat, 01 Jun 2019 21:55:37: end of X-cor INFO @ Sat, 01 Jun 2019 21:55:37: #2 finished! INFO @ Sat, 01 Jun 2019 21:55:37: #2 predicted fragment length is 50 bps INFO @ Sat, 01 Jun 2019 21:55:37: #2 alternative fragment length(s) may be 3,50,169,199,439,454,588 bps INFO @ Sat, 01 Jun 2019 21:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.10_model.r WARNING @ Sat, 01 Jun 2019 21:55:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:55:37: #2 You may need to consider one of the other alternative d(s): 3,50,169,199,439,454,588 WARNING @ Sat, 01 Jun 2019 21:55:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:55:37: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:55:38: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:55:38: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:55:38: #1 total tags in treatment: 9432466 INFO @ Sat, 01 Jun 2019 21:55:38: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:55:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:55:39: #1 tags after filtering in treatment: 9432466 INFO @ Sat, 01 Jun 2019 21:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:55:39: #1 finished! INFO @ Sat, 01 Jun 2019 21:55:39: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:55:39: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:55:39: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:55:39: #1 total tags in treatment: 9432466 INFO @ Sat, 01 Jun 2019 21:55:39: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:55:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:55:39: #1 tags after filtering in treatment: 9432466 INFO @ Sat, 01 Jun 2019 21:55:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:55:39: #1 finished! INFO @ Sat, 01 Jun 2019 21:55:39: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:55:40: #2 number of paired peaks: 243 WARNING @ Sat, 01 Jun 2019 21:55:40: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 01 Jun 2019 21:55:40: start model_add_line... INFO @ Sat, 01 Jun 2019 21:55:40: start X-correlation... INFO @ Sat, 01 Jun 2019 21:55:40: end of X-cor INFO @ Sat, 01 Jun 2019 21:55:40: #2 finished! INFO @ Sat, 01 Jun 2019 21:55:40: #2 predicted fragment length is 50 bps INFO @ Sat, 01 Jun 2019 21:55:40: #2 alternative fragment length(s) may be 3,50,169,199,439,454,588 bps INFO @ Sat, 01 Jun 2019 21:55:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.20_model.r WARNING @ Sat, 01 Jun 2019 21:55:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:55:40: #2 You may need to consider one of the other alternative d(s): 3,50,169,199,439,454,588 WARNING @ Sat, 01 Jun 2019 21:55:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:55:40: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:55:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:55:41: #2 number of paired peaks: 243 WARNING @ Sat, 01 Jun 2019 21:55:41: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 01 Jun 2019 21:55:41: start model_add_line... INFO @ Sat, 01 Jun 2019 21:55:41: start X-correlation... INFO @ Sat, 01 Jun 2019 21:55:41: end of X-cor INFO @ Sat, 01 Jun 2019 21:55:41: #2 finished! INFO @ Sat, 01 Jun 2019 21:55:41: #2 predicted fragment length is 50 bps INFO @ Sat, 01 Jun 2019 21:55:41: #2 alternative fragment length(s) may be 3,50,169,199,439,454,588 bps INFO @ Sat, 01 Jun 2019 21:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.05_model.r WARNING @ Sat, 01 Jun 2019 21:55:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:55:41: #2 You may need to consider one of the other alternative d(s): 3,50,169,199,439,454,588 WARNING @ Sat, 01 Jun 2019 21:55:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:55:41: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:56:15: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:56:15: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:56:18: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.10_summits.bed INFO @ Sat, 01 Jun 2019 21:56:33: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (188 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.20_summits.bed INFO @ Sat, 01 Jun 2019 21:56:33: Done! pass1 - making usageList (6 chroms): 11 millis pass2 - checking and writing primary data (71 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2350755/SRX2350755.05_summits.bed INFO @ Sat, 01 Jun 2019 21:56:37: Done! pass1 - making usageList (6 chroms): 7 millis pass2 - checking and writing primary data (694 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。